Expression profiling using cDNA arrays is becoming a powerful tool for the analysis of gene expression and regulation. Such methodology allows the abundances of thousands of transcripts to be followed simultaneously. This allows the discovery of patterns in gene expression and the association of genes with phenomena and formulation of new regulatory hypotheses on a grand scale. However, a number of important gene transcription variables are not captured in the measurement of steady state mRNA abundance, such as transcriptional vs. post-transcriptional control and immediate-early vs. delayed control. The author states that these types of control mechanisms can be investigated by adapting nuclear run-off assays to the array format. The author predicts that this general approach could significantly enhance the ability to interpret transcript abundance data in existing and future expression profiling databases.